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Title: Molecular events of apical bud formation in white spruce      
dateReleased:
12-01-2010
description:
Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce (Picea glauca [Moench] Voss.), a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for ABA, cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce. Shoot tips (terminal buds), needles, and secondary stems were collected from two-year-old white spruce plants over a 10-week time course of 0, 1, 3, 7, 14, 28, and 70 days after switching from 6 to 8 weeks of long daylight photoperiods (LD; 16 hours of light and 8 hours of dark) to short daylight photoperiods (SD; 8 hours of daylight and 16 hours of dark). Remaining plants were kept in short days for an additional 8-15 weeks, and then transferred to low temperature (LT; 2°C to 4°C) for 3 to 4 weeks with continuing SD prior to harvest. Another set of plants was grown and harvested under the same conditions as described above, but remained in LD at all times. Four sets of dye-swap design microarray experiments were conducted. The first set of experiments (samples 1-7) studied the SD time course of buds development. Terminal buds from each time point (1d, 3d, 7d, 14d, 28d, and 70d) and LT were co-hybridized with actively growing shoot tips (0d). The same time point comparison (without LT) of shoot tips from LD-treated trees was carried out as the second set of experiments (samples 8-13). The third experiment (samples 14-20) denoted a separate LD/SD comparison at seven different time points (0d, 1d, 3d, 7d, 14d, 28d, and 70d), and the last experiment (samples 21-26) compared SD shoot tips, needles, and secondary stems with each of the other tissues at 14d and 70d. In each experiment, four biological replicates were used, with two replicates representing the dye-swaps.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-23519
refinement:
raw
alternateIdentifiers:
23519
keywords:
functional genomics
dateModified:
05-02-2014
availability:
available
types:
gene expression
name:
Picea glauca
ID:
A-GEOD-10754
name:
Arborea spruce 11K cDNA microarray
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-23519/E-GEOD-23519.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-23519/E-GEOD-23519.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23519
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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